We identified a novel protein, designated Thap11 (Thanatos-associated protein 11) in hES cells. Thap11 is an inhibitor of differentiation in ES cells. In contrast to most other factors, Thap11 seems to be directly involved with both, transcriptional control and epigenetic modification. Thapl 1 has a putative DMA-binding domain that shows significant similarity to the DMA-binding domain of the Drosophila P element (a DMA transposon). This suggested that, like the P element, Thapl 1 might act as a site-specific transcriptional modulator, a possibility we subsequently confirmed. Interestingly, one of the genes most strikingly upregulated by Thapl 1 in ES cells is Suz12 (Suppressor of Zeste 12, epigenetic modifier that suppresses differentiation in hES cells). In addition Thapl 1 interacts with DMA methyltransferase like protein 3 (DnmtSL), and has its own NAD+-dependent histone deacetylase (HDAC) activity, making it a novel HDAC in its own right. Our overall hypothesis is that Thapl 1 plays a critical role in controlling self-renewal of hES cells by blocking differentiation. To test this hypothesis will (a) analyze how Thapl 1 controls the expression of Suz12 and identify additional target genes of Thapl 1; knowledge of these genes (including Suz12) is critical since they are part of the transcriptional network that controls the undifferentiated state (pluripotency) of hES cells; (b) dissect the relationship between Thapl 1 and DnmtSL; we will study how Thapl 1 interacts with DnmtSL and if this modulates site-specific DMA methylation of genes (Suz12 and others); (c) analyze the NAD+-dependent HDAC activity of Thapl 1. This information will allow us to modulate Thapl 1's HDAC activity, an effect that in turn should help control differentiation of hES cells if our primary Hypothesis is correct. Since Thapl 1 acts as a transcriptional factor and is also involved in at least two epigenetic mechanisms, DNA methylation and histone deacetylation, it may represent an important link between transcriptional control and epigenetics in hES cells. Specific genetic and pharmacologic interventions targeting Thapl1 function may allow control of self-renewal and differentiation of hES cells.